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<ul>
<ul>
<li class="toclevel-1"><a href="#chain">
<li class="toclevel-1"><a href="#chain">
<span class="tocnumber">1</span> <span class="toctext">Step1 温度感受性リポソームの破壊Disruption of temperature sensitive liposomes</span></a></li>
<span class="tocnumber">1</span> <span class="toctext">Step1 Disruption of temperature sensitive liposomes</span></a></li>
<ul>
<ul>
<li class="toclevel-2"><a href="#bending">
<li class="toclevel-2"><a href="#bending">
<span class="tocnumber">1-1</span> <span class="toctext">Disruption of temperature sensitive liposomes温度感受性リポソームを破壊する実験</span></a></li>
<span class="tocnumber">1-1</span> <span class="toctext">Disruption of temperature sensitive liposomes</span></a></li>
</ul>
</ul>
<li class="toclevel-1"><a href="#Flower">
<li class="toclevel-1"><a href="#Flower">
<span class="tocnumber">2</span> <span class="toctext">Step2 Liposome disruption induced by attachment of key DNA with anchor DNA DNAによる連鎖的リポソームの破壊</span></a></li>
<span class="tocnumber">2</span> <span class="toctext">Step2 Liposome disruption induced by attachment of key DNA with anchor DNA</span></a></li>
<ul>
<ul>
<li class="toclevel-2"><a href="#sensing">
<li class="toclevel-2"><a href="#sensing">
<span class="tocnumber">2-1</span> <span class="toctext">DNA origami approach DNAオリガミによるアプローチ</span></a></li>
<span class="tocnumber">2-1</span> <span class="toctext">DNA Origami approach </span></a></li>
<ul>
<ul>
<li class="toclevel-2"><a href="#5">
<li class="toclevel-2"><a href="#5">
<span class="tocnumber">2-1-1</span> <span class="toctext">Making DNA origami デザインしたDNAオリガミの作製</span></a></li>
<span class="tocnumber">2-1-1</span> <span class="toctext">Making DNA Origami</span></a></li>
<li class="toclevel-2"><a href="#6">
<li class="toclevel-2"><a href="#6">
<span class="tocnumber">2-1-2</span> <span class="toctext">Labeling DNA origami with fluorescent-tagged DNAs DNAオリガミに蛍光付きDNAがハイブリしていることの確認実験</span></a></li>
<span class="tocnumber">2-1-2</span> <span class="toctext">Labeling DNA Origami with fluorescent-tagged DNA</span></a></li>


<li class="toclevel-2"><a href="#7">
<li class="toclevel-2"><a href="#7">
<span class="tocnumber">2-1-3</span> <span class="toctext">Disrupting liposomes by DNA origami DNAオリガミによりリポソームを破壊する実験</span></a></li>
<span class="tocnumber">2-1-3</span> <span class="toctext">Disruption of liposomes by DNA Origami</span></a></li>
<li class="toclevel-2"><a href="#8">
<li class="toclevel-2"><a href="#8">
<span class="tocnumber">2-1-4</span> <span class="toctext">Confirming sequence specificity of DNA DNAによる配列特異性を証明する実験</span></a></li>
<span class="tocnumber">2-1-4</span> <span class="toctext">Confirming sequence specificity of DNA</span></a></li>
</ul>
</ul>
<li class="toclevel-1"><a href="#9">
<li class="toclevel-1"><a href="#9">
<span class="tocnumber">2-2</span> <span class="toctext">Flower DNA approachフラワーミセルによるアプローチ</span></a></li>
<span class="tocnumber">2-2</span> <span class="toctext">Flower DNA approach</span></a></li>
<ul>
<ul>
<li class="toclevel-2"><a href="#10">
<li class="toclevel-2"><a href="#10">
<span class="tocnumber">2-2-1</span> <span class="toctext">Confirming the formation of the loop structure by SPR SPRによるループ構造の確認</span></a></li>
<span class="tocnumber">2-2-1</span> <span class="toctext">Confirming the formation of the loop structure by SPR</span></a></li>
<li class="toclevel-2"><a href="#11">
<li class="toclevel-2"><a href="#11">
<span class="tocnumber">2-2-2</span> <span class="toctext">Disrupting liposomes by Flower DNAsフラワーミセルによりリポソームを破壊する実験</span></a></li>
<span class="tocnumber">2-2-2</span> <span class="toctext">Disruption of liposomes by Flower DNAflu</span></a></li>
<li class="toclevel-2"><a href="#12">
<li class="toclevel-2"><a href="#12">
<span class="tocnumber">2-2-3</span> <span class="toctext">Confirming sequence specificity of DNA DNAによる配列特異性を証明する実験</span></a></li>
<span class="tocnumber">2-2-3</span> <span class="toctext">Confirming sequence specificity of DNA</span></a></li>




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</td></tr></table>


<h3>1 Step1 Disruption of temperature sensitive liposomes温度感受性リポソームの破壊</h3>
<h3>1 Step1 Disruption of temperature sensitive liposomes</h3>
<h4>1-1Disrupting temperature sensitive liposomes温度感受性リポソームを破壊する実験</h4>
<h4>1-1Disruption of temperature sensitive liposomes</h4>
<h6>Purpose</h6>
<h6>Purpose</h6>
In our project, we adopt liposomes conjugated with NIPAM polymer (temperature sensitive liposomes) as initiators that sense environmental change (temperature increase).  
In our project, we adopt liposomes conjugated with NIPAM polymer (temperature sensitive liposomes) as initiators that sense environmental change (temperature increase). <br>
We confirm the initial liposomes with NIPAM break with temperature increase.私たちのプロジェクトでは外部刺激を感知するイニシエーターの一例としてニッパム修飾したリポソーム（温度感受性リポソーム）を使用する。そのため、温度上昇によりニッパム修飾のリポソームが割れること実験により確認する。<br>
We confirm that the initial liposomes with NIPAM break with temperature increase.<br>
<br>
<br>


<h6>Method</h6>
<h6>Method</h6>
We used Egg PC for the lipids and L paraffin for the buffer. Vortex process was applied to make liposomes.
We used Egg PC for the lipids and L paraffin for the buffer. Vortex process was applied to make liposomes.<br>
Then we added NIPAM (dissolved in chloroform) into the liposomes in the mass ratio of chloroform: liposome =???.
Then we added NIPAM (dissolved in chloroform) into the liposomes.<br>
The liposomes were observed on the slide glass with a phase-contrast microscopy.  
The liposomes were observed on the slide glass with a phase-contrast microscopy. <br>
After confirming the formation of the liposomes, we put a petri dish with hot water inside on the slide glass to increase the temperature.
After confirming the formation of the liposomes, we put a petri dish with hot water inside on the slide glass to increase the temperature.<br>
脂質にはEggPC、バッファーにはLパラフィン？を使用し、ボルテックス法によりリポソームを作製した。<br>
リポソームにNIPAM (in クロロホルム)を質量比？？？の割合で加えた。<br>
スライドガラスを作製し、位相差顕微鏡でリポソームがあることを確認した。<br>
リポソームが確認できたら、スライドガラスの上にお湯を乗せて温度を上げた。<br>
Protocol<br>
Protocol<br>
（対応するプロトコルへのリンク）<br>
（対応するプロトコルへのリンク）<br>


<h6>Result</h6>
<h6>Result</h6>
Fig.1 shows liposomes before the temperature increase.
Fig.1 shows liposomes before the temperature increase. <br>
温度を上げる前のリポソームの状態は図１のようになった。<br>


<img src="http://openwetware.org/images/8/89/Snap_20131018_193341_8127.jpg"><br>
<img src="http://openwetware.org/images/8/89/Snap_20131018_193341_8127.jpg"><br>
Fig.1 Liposomes with NIPAM before the temperature increase図１　温度を上げる前のニッパム付きのリポソーム<br>
Fig.1 Liposomes with NIPAM before the temperature increase<br>
 
<br>
Figure 2 shows the state after the temperature increase by putting a petri dish with hot water inside on the slide glass. The view sight in Fig.2 was the same as that in Figure 1.  
Figure 2 and 3 shows the state after the temperature increase by putting a petri dish with hot water inside on the slide glass. The view sight in Fig.2 and 3 was the same as that in Figure 1. <br>
No liposome and only a rough background were observed in Fig.2. Even after the focus shift, no liposome was seen.
Only a rough background and no liposome were observed in Fig.3. Even after focus shifts, no liposome was seen.<br>
スライドガラスにお湯を乗せて温度を上昇させた後のリポソームの様子は以下図２、図３のようになった。観察しているリポソームは図１のものと同じである。まず、図２のようにバックグラウンドがザラザラになって、しばらくすると図３のようにリポソームが確認できなくなった。ピントを調節してもリポソームは確認できなかった。<br>
 
<img src="http://openwetware.org/images/2/21/Snap_20131018_193358_8128.jpg"><br>
<img src="http://openwetware.org/images/2/21/Snap_20131018_193358_8128.jpg"><br>
図２　温度上昇後のニッパム付きのリポソーム<br>
Fig.2 the state after the temperature increase<br>
Fig.2 the state after the temperature increase
<img src="http://openwetware.org/images/6/63/Snap_20131018_193431_8129.jpg"><br>
<img src="http://openwetware.org/images/6/63/Snap_20131018_193431_8129.jpg"><br>
図３　温度を上昇させた後のニッパム付きのリポソームが消えた様子<br>
Fig.3 the state after the temperature increase<br>
Fig.2 the state after the temperature increase


<h6>Discussion</h6>
<h6>Discussion</h6>
As liposomes present in Fig.1 disappeared in Fig.2, liposomes with NIPAM were likely to have broken. On the other hand, some liposomes were still present even after the temperature increase. This is probably because they are multi-lamella liposomes (liposomes that consist of many lipid bilayers). Multi-lamella liposomes are more difficult to break than uni-lamella ones. Therefore, we suppose that liposomes that were present in Fig.1 but disappeared in Fig.2 were uni-lamella ones.
As liposomes present in Fig.1 disappeared in Fig.3, liposomes with NIPAM were likely to have burst. <br>
図１で見えていたリポソームが、図２，３のように消えてしまったのでニッパム付きのリポソームが割れたと考えられる。しかし、リポソームによっては温度を上げた後も残っているものがいくつか確認できた。これはリポソームがマルチラメラ（脂質二重膜が複数重なっているもの）になっているものと考えられ、脂質二重膜が単一層のユニラメラよりも割れにくいからだと考えられる。上記図１，２，３で定点観察したリポソームはユニラメラであると考えられる。<br>
On the other hand, some liposomes were still present even after the temperature increase. This is probably because they are multi-lamella liposomes (liposomes that consist of many lipid bilayers). Multi-lamella liposomes are more difficult to break than uni-lamella ones. Therefore, we suppose that liposomes that were present in Fig.1 but disappeared in Fig.3 were uni-lamella ones.<br>


<h3>2 Step2 DNAによる連鎖的リポソームの破壊</h5>
<h3>2 Step2 Liposome disruption induced by attachment of key DNA with anchor DNA</h5>
<h4>2-1 DNAオリガミによるアプローチ</h4>
<h4>2-1 DNA Origami approach</h4>
<h5>2-1-1 デザインしたDNAオリガミの作製</h5>
<h5>2-1-1 Making DNA Origami</h5>
<h6>Purpose</h6>
<h6>Purpose</h6>
In our project, we used DNA origami as triggers to break liposomes. We designed a rectangular DNA origami with a chipped edge and tried to make it.<br>
In our project, we use DNA Origami as Key DNA to break liposomes. We design rectangular DNA Origami with a chipped edge and try to make it.<br>
   
   
<h6>Method</h6>
<h6>Method</h6>
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<h6>Result</h6>
<h6>Result</h6>
We confirmed that our DNA origami was well formed by AFM (Atomic Force Microscope) (Fig.1).<br>
We confirmed that our DNA Origami was well formed by AFM (Atomic Force Microscope) (Fig.4).<br>
<Img Src="http://openwetware.org/images/d/d9/Outsideafm2.png"> <br>
<Img Src="http://openwetware.org/images/d/d9/Outsideafm2.png"> <br>
Fig.1 AFM image of DNA origami (M13: 4nM, staples:20nM)<br>
Fig.4 AFM image of DNA Origami (M13: 4nM, staples:20nM)<br>
<br>
<br>


<h6>Discussion</h6>
<h6>Discussion</h6>
Just like our design, rectanglar origamis with chipped edges were observed.
Just like our design, rectangular DNA Origami with a chipped edge was observed.<br>


<h5>2-1-2 DNAオリガミに蛍光付きDNAがハイブリしていることの確認実験</h5>
<h5>2-1-2 Labeling DNA Origami with fluorescent-tagged DNA</h5>
<h6>Purpose</h6>
<h6>Purpose</h6>
If the origami is fluorescently labeled, it is much easier to observe the effect of DNA origami on liposomes. So we labeled our origami by hybridizing it with fluorescent tagged DNAtrands.<br><br>
If Origami is fluorescently labeled, it is much easier to observe the effect of DNA Origami on liposomes. So we labeled our Origami by hybridizing it with fluorescent-tagged DNA strand.<br><br>


<h6>Method</h6>
<h6>Method</h6>
Our DNA origami has many staples that can bind to fluorescent tagged DNA for labeling. We mixed fluorescent tagged DNA together with DNA origami staples in annealing solution.<br>
Our DNA Origami has many staples that can bind to fluorescent-tagged DNA for labeling. We mixed fluorescent-tagged DNA together with DNA Origami staples in annealing solution.<br>
In addition, to see if the origami binds to the fluorescent tagged DNA in shorter time, we added the fluorescent tagged DNA into control annealing solution, which contained no fluorescent tagged DNA, and left it for 40 minutes.<br>
In addition, to see if the Origami binds to the fluorescent-tagged DNA in a shorter time, we added the fluorescent-tagged DNA into the control annealing solution, which had contained no fluorescent-tagged DNA, and left it for 40 minutes.<br>
To see the origami was well labeled with fluorescent molecules, we used electrophoresis. <br>
To see the Origami was well labeled with fluorescent molecules, we used electrophoresis. <br>
Electrophoresis was conducted with a 1% agarose gel, CV100V for 50 minutes.<br>
Electrophoresis was conducted with a 1% agarose gel, CV100V for 50 minutes.<br>
<A href="http://openwetware.org/wiki/Biomod/2013/Sendai/protocol">Protocol</A><br>
<A href="http://openwetware.org/wiki/Biomod/2013/Sendai/protocol">Protocol</A><br>
<br>
<br>
By scanning a gel before staining, we can see only the bands of DNAtructures with fluorescent molecules; scanning a gel after staining, we can see the bands of all DNAtructures. So we scanned a gel before and after staining (we scanned both a non-stained and a stained gel). <br>
By scanning a gel before staining, we can see only the bands of DNA structures with fluorescent molecules; scanning a gel after staining, we can see the bands of all DNA structures. So we scanned a gel before and after staining (we scanned both a non-stained and a stained gel). <br>
First we saw the bands of our origami in a non-stained gel. Then, we compared the bands with those in a stained gel. If the bands of origami in a non-stained gel were at the same height as those in a stained gel, we can say that our origami is successfully fluorescently labeled.<br>
First we saw the bands of our Origami in a non-stained gel. Then, we compared the bands with those in a stained gel. If the bands of Origami in a non-stained gel were at the same height as that in a stained gel, we can say that our Origami was successfully fluorescently labeled.<br>
<br>
<br>


<h6>Result</h6>  
<h6>Result</h6>  
In a non-stained gel (Fig.2), only bands in lane 3 and 4 from the left (*Ori, **Ori) can be seen. They are fluorescent labeled structures. In addition, as they gave the same result, 40 minutes is long enough for fluorescent labeling.<br>
In a non-stained gel (Fig.5), only bands in lane 3 and 4 from the left (*Ori, **Ori) can be seen. They are fluorescently labeled structures. In addition, as they gave the same result, 40 minutes is long enough for fluorescently labeling.<br>
<Img Src="http://openwetware.org/images/5/58/S_Outside-gel-3.2.png" width="300"><br>
<Img Src="http://openwetware.org/images/5/58/S_Outside-gel-3.2.png" width="300"><br>
Fig.2 Non-stained gel image: only bands in two lanes can be seen. From the left, they are DNA origami with fluorescent molecules in pre-annealing (Ori*), and DNA origami with fluorescent molecules in post-annealing (Ori**)<br>
Fig.5 Non-stained gel image: only bands in two lanes can be seen. From the left, they are DNA Origami with fluorescent molecules in pre-annealing (Ori*), and DNA Origami with fluorescent molecules in post-annealing (Ori**)<br>
<br>
<br>
In a stained gel (Fig.3), marker (lane 1) had the longest DNAtrand of 20kb. Comparing this and M13mp18 (lane 2) with annealed DNA origamis (lane 3,4,5), the bands of the origamis are at the higher position. Therefore, we concluded that in lane3~5, DNA origami structure made of M13 and staples were made as we had expected. <br>
In a stained gel (Fig.6), marker lane (lane 1) had the longest DNA strand of 20kb. Comparing this band and the band of M13mp18 (lane 2) with annealed DNA Origami (lane 3,4,5), the bands of the Origami are at the higher position. Therefore, we concluded that in lane3~5, DNA Origami structure was made as we had expected. <br>
We considered that the bands in lane3~5 are seen as if they were diffused, just because our origami has many staples binding to the fluorescent tagged DNA, and each origami attaches to different number of them, and its molecular weight varies.<br>
We considered that the bands in lane3~5 are seen as if they were diffused, just because our Origami has many staples binding to the fluorescent-tagged DNA, and each Origami attaches to different number of them, and its molecular weight varies.<br>
<Img Src="http://openwetware.org/images/2/2d/S_Outside-gel-2.2.png" width="300"> </br>
<Img Src="http://openwetware.org/images/2/2d/S_Outside-gel-2.2.png" width="300"> </br>
Fig.3 Stained gel image: from the left, marker, M13mp18, Ori*, Ori**, and DNA origami with no fluorescent molecule (Ori)<br>
Fig.6 Stained gel image: from the left, marker, M13mp18, Ori*, Ori**, and DNA Origami with no fluorescent molecule (Ori)<br>
<br>
<br>


<h6>Discussion</h6>
<h6>Discussion</h6>
Combining the results of Fig.2 and 3, the fluorescent labeled bands in lane3 and 4 in Fig.2 are at the same height as those of DNA origami in Fig.3. Thus, we concluded our origami was successfully fluorescently labeled.<br>
Combining the results of Fig.5 and 6, the fluorescently labeled bands in lane3 and 4 in Fig.5 are at the same height as those of DNA Origami in Fig.6. Thus, we concluded our Origami was successfully fluorescently labeled.<br>
<br>
<br>


<h5>2-1-3 DNAオリガミによりリポソームを破壊する実験<h5>
<h5>2-1-3 Disrupting liposomes by DNA Origami<h5>
<h6>Purpose</h6>
<h6>Purpose</h6>
To break liposome with our origami, first we investigated how our DNA origami affected liposomes.<br>
To break liposomes with our Origami, first we investigate how our DNA Origami affect liposomes.<br>
<br>
<br>
<h6>Principle</h6>
<h6>Principle</h6>
To break liposomes with our origami, many origamis have to hybridize with the surface of liposomes.<br>
To break liposomes with our Origami, a lot of Origami has to hybridize to the surface of the liposomes.<br>
To begin with, we added cholesterol-conjugated single-stranded DNA (in the rest of this document, referred to as Anchored DNA) into liposomes, and made them float on the surface. If the Anchored DNA have a complementary part to our origami, the origami is expected to hybridize with the surface. In this way, many origamis would hybridize with liposome via Anchored DNA.<br>
To begin with, we added cholesterol-conjugated single-stranded DNA (in the rest of this document, referred to as Origami-anchor DNA) into liposomes, and made it float on the surface. The Origami-anchor DNA has a complementary part to our Origami, so the Origami is expected to hybridize to Origami-anchor DNA on the liposomes. In this way, lots of Origami would hybridize to liposomes via Origami-anchor DNA.<br>
<br>
<br>
<h6>Method</h6>
<h6>Method</h6>
We added Anchored DNA into liposomes at the final concentration of 0.018, 0.069, 1.8, and 6.9µM. Then we observed the samples with a phase microscope. Next, adding fluorescently labeled DNA origamis into the above liposomes, we saw if some change would happen with a fluorescent microscope.<br>
We added Origami-anchor DNA into liposomes at the final concentration of 0.018, 0.069, 1.8, and 6.9µM. Then we observed the samples with a phase microscope. <br>
Next, adding fluorescently labeled DNA Origami into the above liposomes, we saw if some change would happen with a fluorescent microscope.<br>
<A href="http://openwetware.org/wiki/Biomod/2013/Sendai/protocol">Protocol</A><br>
<A href="http://openwetware.org/wiki/Biomod/2013/Sendai/protocol">Protocol</A><br>
<br>
<br>
<h6>Result</h6>
<h6>Result</h6>
In all four conditions, liposomes were observed with a phase microscope. We confirmed the formation of multilamella liposomes (Fig.4~7).<br>
In all four conditions, liposomes were observed with a phase microscope. We confirmed the formation of multi-lamella liposomes (Fig.7~10).<br>
<br>
<br>


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<Img Src="http://openwetware.org/images/7/72/Lipofig4.png" width="400"></br>
<Img Src="http://openwetware.org/images/7/72/Lipofig4.png" width="400"></br>
Fig.4 Phase microscope image of liposomes (cholesterol-conjugated DNA: 0.018µM)<br>
Fig.7 Phase microscope image of liposomes (Origami-anchor DNA: 0.018µM)<br>
<br>
<br>
<Img Src="http://openwetware.org/images/d/d0/Lipofig5.png" width="400"></br>
<Img Src="http://openwetware.org/images/d/d0/Lipofig5.png" width="400"></br>
  Fig.5 Phase microscope image of liposomes (cholesterol-conjugated DNA: 0.069µM)<br>
  Fig.8 Phase microscope image of liposomes (Origami-anchor DNA: 0.069µM)<br>
<br>
<br>
<Img Src="http://openwetware.org/images/d/de/Lipofig6.png" width="400"></br>
<Img Src="http://openwetware.org/images/d/de/Lipofig6.png" width="400"></br>
  Fig.6 Phase microscope image of liposomes (cholesterol-conjugated DNA: 1.8µM)<br>
  Fig.9 Phase microscope image of liposomes (Origami-anchor DNA: 1.8µM)<br>
<br>
<br>
<Img Src="http://openwetware.org/images/d/d7/Lipofig7.png" width="400"></br>
<Img Src="http://openwetware.org/images/d/d7/Lipofig7.png" width="400"></br>
  Fig.7 Phase microscope image of liposomes (cholesterol-conjugated DNA: 6.9µM)<br>
  Fig.10 Phase microscope image of liposomes (Orgami-anchor DNA: 6.9µM)<br>
<br>
<br>
Adding fluorescently labeled DNA origamis into the above liposomes, we saw if some change would happen with a fluorescent microscope.<br>
Adding fluorescently labeled DNA Origami into the above liposomes, we saw if some change would happen with a fluorescent microscope.<br>
When the concentration of Anchored DNA was 0.018, 0.069µM, many gleaming (in green color) liposomes were observed. We confirmed that the fluorescently labeled origamis well hybridized with the liposomal surface (Fig.8,9,10). <br>
When the concentration of Origami-anchor DNA was 0.018, 0.069µM, many gleaming (in green color) liposomes were observed. We confirmed that the fluorescently labeled Origami well hybridized to the liposomal surface (Fig.11,12,13). <br>
<table>
<table>
  <tr>
  <tr>
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  </tr>
  </tr>
</table>
</table>
Fig.8,9 fluorescent microscope image of liposomes (cholesterol-conjugated DNA: 0.018µM)<br>
Fig.11,12 fluorescent microscope image of liposomes (Origami-anchor DNA: 0.018µM)<br>
<Img Src="http://openwetware.org/images/b/b4/Lipofig10.png" width="400"></br>
<Img Src="http://openwetware.org/images/b/b4/Lipofig10.png" width="400"></br>
Fig.10 fluorescent microscope image of liposomes (cholesterol-conjugated DNA: 0.069µM)<br>
Fig.13 fluorescent microscope image of liposomes (Origami-anchor DNA: 0.069µM)<br>
<br>
<br>
On the other hand, when the concentration of Anchored DNA was 1.8µM, few gleaming liposomes could be seen with a fluorescent microscope (Fig.11). This result indicates the possibility that liposomes have broken.<br>
On the other hand, when the concentration of Origami-anchor DNA was 1.8µM, few gleaming liposomes could be seen with a fluorescent microscope (Fig.14). This result indicates the possibility that liposomes have broken.<br>
<Img Src="http://openwetware.org/images/1/18/Lipofig11.png" width="400"></br>
<Img Src="http://openwetware.org/images/1/18/Lipofig11.png" width="400"></br>
Fig.11 fluorescent microscope image of liposomes (cholesterol-conjugated DNA: 1.8µM)<br>
Fig.14 fluorescent microscope image of liposomes (Origami-anchor DNA: 1.8µM)<br>
<br>
<br>
When the concentration of Anchored DNA is 6.9µM, some liposomes were gleaming and others distorted, forming networks (Fig.12).<br>
When the concentration of Origami-anchor DNA is 6.9µM, some liposomes were gleaming and others distorted, forming networks (Fig.15).<br>
   
   
<Img Src="http://openwetware.org/images/8/88/Lipofig12.png" width="400"></br>
<Img Src="http://openwetware.org/images/8/88/Lipofig12.png" width="400"></br>
  Fig.12 fluorescent microscope image of liposomes (cholesterol-conjugated DNA: 6.9µM)<br>
  Fig.15 fluorescent microscope image of liposomes (Origami-anchor DNA: 6.9µM)<br>
<br>
<br>
<h6>Discussion</h6>
<h6>Discussion</h6>
From these results, we put forward the following hypothesis about the interaction of DNA origami and liposomes.<br>
From these results, we put forward the following hypothesis about the interaction of DNA Origami and liposomes.<br>
When the concentration of Anchored DNA is low (0.018, 0.069µM), DNA origamis hybridize with the surface of the liposomes relatively stablely. When the concentration is middle (1.8µM), more DNA origamis hybridizes with the surface and place stress on it. Then, liposomes become fragile and easy to break. When the concentration is high (6.9µM), some liposomes exist individually, and others form networks via Anchored DNA and DNA origami complexes.<br>
When the concentration of Origami-anchor DNA is low (0.018, 0.069µM), DNA Origami hybridizes to the surface of liposomes relatively stablely. When the concentration is middle (1.8µM), more DNA Origami hybridizes to the surface and loads on it. The liposomes become fragile and easy to break. When the concentration is high (6.9µM), some liposomes exist individually, and others form networks via Origami-anchor DNA and DNA Origami complex.<br>
<Img Src="http://openwetware.org/images/7/7c/Experimentinsidefig.png"><br>
<Img Src="http://openwetware.org/images/7/7c/Experimentinsidefig.png"><br>
<br>
<br>
According to this hypothesis, when the concentration of Anchored DNA is 1.8µM, DNA origami breaks liposomes. Therefore, in the following experiment, we checked if DNA origami would break liposomes at this concentration of Anchored DNA.<br>
According to this hypothesis, when the concentration of Origami-anchor DNA is 1.8µM, DNA Origami breaks liposomes. <br>
<br>
<br>
<br>
<br>
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-->
-->


<h5>2-1-4 DNAによる配列特異性を証明する実験</h5>
<h5>2-1-4 Confirming sequence specificity of DNA </h5>
<h6>Purpose</h6>
<h6>Purpose</h6>
In this project, we focus on the sequence specificity of DNA. Utilizing this sequence specificity, we aim to choose liposomes that will be broken by trigger DNAs, induce chain-reactive liposomal disruption by some trigger DNAs, and make connections between liposomes.
In this project, we adopt DNA for the Key of chain reaction because DNA has a significant characteristic: sequence specificity. Utilizing this sequence specificity, we aim to select liposomes that will be broken by Key DNA, induce chain-reactive liposomal disruption by some Key DNA, and make connections between liposomes.<br>
Corresponding to the liposomes, we arrange two kinds of anchor DNAs of different sequences and attach the anchors to the liposomes. Then we mix both kinds of liposomes together.  
Corresponding to the liposomes, we arrange two kinds of Origami-anchor DNA of different sequences and attach the anchor to the liposomes. Then we mix both kinds of liposomes together. <br>
Into the mixture, trigger DNAs for just one kind of liposomes are added. We confirm that the trigger DNAs break only the corresponding kind of liposomes.
Into the mixture, Key DNA for just one kind of liposomes is added. We confirm that the Key DNA breaks only the corresponding kind of liposomes.<br>
このプロジェクトにおいてリポソームをDNAで割る理由は、DNAの配列特異性を利用して割れるリポソーム間に関係性を持たせるためである。そこで配列の異なる２種類のDNAを生やしたリポソームを用意して片方だけに相補なDNAを加え、２種類のリポソームのうちDNAが相補になっている片方のリポソームだけが破壊されることを確かめた。<br>
<br>


<h6>Method</h6>
<h6>Method</h6>
We made two kinds of liposomes: liposomeA and liposomeB by water-in-oil emulsion process. LiposomeA contains GFP (Green Fluorescent Protein) inside, and liposomeB has Rhodamine (red fluorescent dye) in itself. 内部にGFP（緑の蛍光）を含んだリポソームAとローダミン（赤の蛍光）を含んだリポソームBの２種類のリポソームを、界面通過法により作製する。どちらのリポソームも
We made two kinds of liposomes: liposomeA and liposomeB by water-in-oil emulsion process. LiposomeA contains GFP (Green Fluorescent Protein) inside, and liposomeB has Rhodamine (red fluorescent dye) in itself. <br>
<!--脂質の組成は？-->
<!--脂質の組成は？-->
<br>
<br>
The anchor DNA for liposome A has the sequence of 5'-CCAGAAGACG-chol-3'. The anchor for liposome B has the sequence of 5'-TCCACTAACG-chol-3'. Both anchors (cholesterol-conjugated) were mixed with the corresponding liposomes.
Origami-anchor DNA for liposome A has the sequence of 5'-CCAGAAGACG-chol-3'. The anchor for liposome B has the sequence of 5'-TCCACTAACG-chol-3'. Both Origami-anchor DNA was mixed with the corresponding liposomes.<br>
Each liposome was centrifuged for one minute to remove the excess anchors.
Each liposome was centrifuged for one minute to remove the excess Origami- anchor DNA.<br>
Then we mixed 1µl of each liposome and observed it with a phase-contrast microscope.
Then we mixed 1µl of each liposome and observed it with a phase-contrast microscope.
リポAには5'-CCAGAAGACG-chol-3'の配列を持つコレステロール付きのDNAをリポソームBには配列5'-TCCACTAACG-chol-3'をもつコレステロール付きのDNAを振り掛けた。<br>
Next, 4µl refined DNA Origami was added to the mixture (of liposomeA and B). The sample was also observed with a phase-contrast microscope. <br>
1分間遠心分離器にかけて、リポソームにくっつかなったコレステロール付きDNAとリポソームを分離する。<br>
リポソームAとリポソームBが入っているリポソームを1μℓずつ混合し、位相差顕微鏡で観察した。<br>
Next, 4µl refined DNA origami was added to the mixture (of liposomeA and B). The sample was also observed with a phase-contrast microscope.  
精製したDNAオリガミ
<!--蛍光ついている？？-->
<!--蛍光ついている？？-->
を4μℓをリポソームA,Bの混合サンプルに加え、位相差顕微鏡で観察した。<br>
Protocol<br>
Protocol<br>
（対応するプロトコルへのリンク）<br>
（対応するプロトコルへのリンク）<br>


<h6>Result</h6>
<h6>Result</h6>
Fig.17 is the phase-contrast microscope image of the mixture of liposome A and B before the addition of trigger DNA origami.  
Fig.16 is the phase-contrast microscope image of the mixture of liposome A and B before the addition of Key DNA Origami.  
トリガーのDNA折り紙を入れていないリポソームA、Bの混合サンプルを位相差顕微鏡で観察すると、図17のようになった<br>
<br>
<img src="http://openwetware.org/images/6/68/LegA%2BB_10.jpg"><br>
<img src="http://openwetware.org/images/6/68/LegA%2BB_10.jpg"><br>
Fig.17 Phase contrast microscope image of the mixture of liposome A (Green) and B (Red)
Fig.16 Phase contrast microscope image of the mixture of liposome A (Green) and B (Red)
図17 GFPとローダミン染色した2種類のリポソーム混合サンプルの位相差顕微鏡画像
 
<h6>Discussion</h6>
<h6>Discussion</h6>
 
(要加筆)
<h4>2-2 フラワーミセルによるアプローチ</h4>
<br>
<h5> 2-2-1 SPRによるループ構造の確認</h5>
<h4>2-2 Flower DNA approach</h4>
<h5> 2-2-1 Confirming the formation of the loop structure by SPR</h5>
<h6>Purpose</h6>
<h6>Purpose</h6>
To break liposomes by flower DNA method, we aim to attach many loop strands to the surface of liposomes. <br>
To break liposomes by flower DNA method, we aim to attach many loop strands to the surface of liposomes. <br>
To achieve this, we adopt the same hybridization method via Anchored DNA as used in i)Bending approach into liposomes: the Anchored DNA has a complementary part to our loop strand and the loop strand is expected to hybridize with liposomes.<br>
To achieve this, we adopt the same hybridization method via Anchored DNA as used in i)Bending approach into liposomes: the Anchored DNA has a complementary part to our loop strand and the loop strand is expected to hybridize to liposomes.<br>
We checked the hybridization of liposomes and Anchored DNA, and that of Anchored DNA and our loop strands. <br>
We checked the hybridization of liposomes and Anchored DNA, and that of Anchored DNA and our loop strands. <br>
<br>
<br>
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<li>3. Inject 10µl Anchored DNA (0.1µM) to SPR</li>
<li>3. Inject 10µl Anchored DNA (0.1µM) to SPR</li>
<li>4. Inject 10µl loop DNA of 40 bp (0.1µM) to SPR</li>
<li>4. Inject 10µl loop DNA of 40 bp (0.1µM) to SPR</li>
<li>5. Inject 10 µl trigger DNA of 40 bp (0.1µM) to SPR</li>
<li>5. Inject 10 µl Key DNA of 40 bp (0.1µM) to SPR</li>
<br>
<br>
<br>
<br>
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<br>
<br>
As the first injection of Anchored DNA caused no change of SPR value, we injected Anchored DNA for two times. <br>
As the first injection of Anchored DNA caused no change of SPR value, we injected Anchored DNA for two times. <br>
Fig 15 shows that SPR value increased after injecting Anchored DNA and loop DNA. Moreover, we should note that after injecting trigger DNAome changes of SPR value were observed.<br>
Fig 15 shows that SPR value increased after injecting Anchored DNA and loop DNA. Moreover, we should note that after injecting Key DNA some changes of SPR value were observed.<br>
<br>
<br>


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<h5>2-2-2フラワーミセルによりリポソームを破壊する実験</h5>
<h5>2-2-2フラワーミセルによりリポソームを破壊する実験</h5>
<h6>Purpose</h6>
<h6>Purpose</h6>
In flower DNA approach, the trigger DNA strands attach to anchor DNAs on liposomes, load on the liposomes, and break them. We confirm the disruption of liposomes   
In flower DNA approach, the Key DNA strand attaches to Flower-anchor DNA on liposomes, load on the liposomes, and break them. We confirm the disruption of liposomes   
フラワーミセルアプローチでは鍵DNAストランドがリポソーム表面に生えているアンカーDNAにハイブリしてリポソームが割れる必要がある。それを確かめるために。
フラワーミセルアプローチでは鍵DNAストランドがリポソーム表面に生えているアンカーDNAにハイブリしてリポソームが割れる必要がある。それを確かめるために。


<h6>Method</h6>
<h6>Method</h6>
We annealed DNA origami with fluorescently-labeled staples.  
We annealed DNA Origami with fluorescently labeled staples.  
Liposomes dyed with Texas Red (fluorescent dye) were prepared, and observed with a fluorescent microscope.  
Liposomes dyed with Texas Red (fluorescent dye) were prepared, and observed with a fluorescent microscope.  
Then we added DNA origami into the liposomes. They were also observed with a fluorescent microscope.
Then we added DNA Origami into the liposomes. They were also observed with a fluorescent microscope.
DNAオリガミに蛍光をハイブリさせたものをアニーリングにより作製する
DNAオリガミに蛍光をハイブリさせたものをアニーリングにより作製する
膜染色（テキサスレッド）したリポソームをつくる
膜染色（テキサスレッド）したリポソームをつくる

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<h2>Experiment</h2>

<table id="toc" class="toc" summary="Contents"><tr><td><div id="toctitle"><h2>Contents</h2></div> <ul> <li class="toclevel-1"><a href="#chain"> <span class="tocnumber">1</span> <span class="toctext">Step1 Disruption of temperature sensitive liposomes</span></a></li> <ul> <li class="toclevel-2"><a href="#bending"> <span class="tocnumber">1-1</span> <span class="toctext">Disruption of temperature sensitive liposomes</span></a></li> </ul> <li class="toclevel-1"><a href="#Flower"> <span class="tocnumber">2</span> <span class="toctext">Step2 Liposome disruption induced by attachment of key DNA with anchor DNA</span></a></li> <ul> <li class="toclevel-2"><a href="#sensing"> <span class="tocnumber">2-1</span> <span class="toctext">DNA Origami approach </span></a></li> <ul> <li class="toclevel-2"><a href="#5"> <span class="tocnumber">2-1-1</span> <span class="toctext">Making DNA Origami</span></a></li> <li class="toclevel-2"><a href="#6"> <span class="tocnumber">2-1-2</span> <span class="toctext">Labeling DNA Origami with fluorescent-tagged DNA</span></a></li>

<li class="toclevel-2"><a href="#7"> <span class="tocnumber">2-1-3</span> <span class="toctext">Disruption of liposomes by DNA Origami</span></a></li> <li class="toclevel-2"><a href="#8"> <span class="tocnumber">2-1-4</span> <span class="toctext">Confirming sequence specificity of DNA</span></a></li> </ul> <li class="toclevel-1"><a href="#9"> <span class="tocnumber">2-2</span> <span class="toctext">Flower DNA approach</span></a></li> <ul> <li class="toclevel-2"><a href="#10"> <span class="tocnumber">2-2-1</span> <span class="toctext">Confirming the formation of the loop structure by SPR</span></a></li> <li class="toclevel-2"><a href="#11"> <span class="tocnumber">2-2-2</span> <span class="toctext">Disruption of liposomes by Flower DNAflu</span></a></li> <li class="toclevel-2"><a href="#12"> <span class="tocnumber">2-2-3</span> <span class="toctext">Confirming sequence specificity of DNA</span></a></li>


</li>


</ul> </li> </ul> </td></tr></table>

<h3>1 Step1 Disruption of temperature sensitive liposomes</h3> <h4>1-1Disruption of temperature sensitive liposomes</h4> <h6>Purpose</h6> In our project, we adopt liposomes conjugated with NIPAM polymer (temperature sensitive liposomes) as initiators that sense environmental change (temperature increase). <br> We confirm that the initial liposomes with NIPAM break with temperature increase.<br> <br>

<h6>Method</h6> We used Egg PC for the lipids and L paraffin for the buffer. Vortex process was applied to make liposomes.<br> Then we added NIPAM (dissolved in chloroform) into the liposomes.<br> The liposomes were observed on the slide glass with a phase-contrast microscopy. <br> After confirming the formation of the liposomes, we put a petri dish with hot water inside on the slide glass to increase the temperature.<br> Protocol<br> （対応するプロトコルへのリンク）<br>

<h6>Result</h6> Fig.1 shows liposomes before the temperature increase. <br>

<img src="http://openwetware.org/images/8/89/Snap_20131018_193341_8127.jpg"><br> Fig.1 Liposomes with NIPAM before the temperature increase<br> <br> Figure 2 and 3 shows the state after the temperature increase by putting a petri dish with hot water inside on the slide glass. The view sight in Fig.2 and 3 was the same as that in Figure 1. <br> Only a rough background and no liposome were observed in Fig.3. Even after focus shifts, no liposome was seen.<br> <img src="http://openwetware.org/images/2/21/Snap_20131018_193358_8128.jpg"><br> Fig.2 the state after the temperature increase<br> <img src="http://openwetware.org/images/6/63/Snap_20131018_193431_8129.jpg"><br> Fig.3 the state after the temperature increase<br>

<h6>Discussion</h6> As liposomes present in Fig.1 disappeared in Fig.3, liposomes with NIPAM were likely to have burst. <br> On the other hand, some liposomes were still present even after the temperature increase. This is probably because they are multi-lamella liposomes (liposomes that consist of many lipid bilayers). Multi-lamella liposomes are more difficult to break than uni-lamella ones. Therefore, we suppose that liposomes that were present in Fig.1 but disappeared in Fig.3 were uni-lamella ones.<br>

<h3>2 Step2 Liposome disruption induced by attachment of key DNA with anchor DNA</h5> <h4>2-1 DNA Origami approach</h4> <h5>2-1-1 Making DNA Origami</h5> <h6>Purpose</h6> In our project, we use DNA Origami as Key DNA to break liposomes. We design rectangular DNA Origami with a chipped edge and try to make it.<br>

<h6>Method</h6> We mixed M13mp18, staples, 5xTAE Mg2+, and mQ in a microtube and annealed it for 2.5 hours.<br> <A href="http://openwetware.org/wiki/Biomod/2013/Sendai/protocol">Protocol</A><br> <br>

<h6>Result</h6> We confirmed that our DNA Origami was well formed by AFM (Atomic Force Microscope) (Fig.4).<br> <Img Src="http://openwetware.org/images/d/d9/Outsideafm2.png"> <br> Fig.4 AFM image of DNA Origami (M13: 4nM, staples:20nM)<br> <br>

<h6>Discussion</h6> Just like our design, rectangular DNA Origami with a chipped edge was observed.<br>

<h5>2-1-2 Labeling DNA Origami with fluorescent-tagged DNA</h5> <h6>Purpose</h6> If Origami is fluorescently labeled, it is much easier to observe the effect of DNA Origami on liposomes. So we labeled our Origami by hybridizing it with fluorescent-tagged DNA strand.<br><br>

<h6>Method</h6> Our DNA Origami has many staples that can bind to fluorescent-tagged DNA for labeling. We mixed fluorescent-tagged DNA together with DNA Origami staples in annealing solution.<br> In addition, to see if the Origami binds to the fluorescent-tagged DNA in a shorter time, we added the fluorescent-tagged DNA into the control annealing solution, which had contained no fluorescent-tagged DNA, and left it for 40 minutes.<br> To see the Origami was well labeled with fluorescent molecules, we used electrophoresis. <br> Electrophoresis was conducted with a 1% agarose gel, CV100V for 50 minutes.<br> <A href="http://openwetware.org/wiki/Biomod/2013/Sendai/protocol">Protocol</A><br> <br> By scanning a gel before staining, we can see only the bands of DNA structures with fluorescent molecules; scanning a gel after staining, we can see the bands of all DNA structures. So we scanned a gel before and after staining (we scanned both a non-stained and a stained gel). <br> First we saw the bands of our Origami in a non-stained gel. Then, we compared the bands with those in a stained gel. If the bands of Origami in a non-stained gel were at the same height as that in a stained gel, we can say that our Origami was successfully fluorescently labeled.<br> <br>

<h6>Result</h6> In a non-stained gel (Fig.5), only bands in lane 3 and 4 from the left (*Ori, **Ori) can be seen. They are fluorescently labeled structures. In addition, as they gave the same result, 40 minutes is long enough for fluorescently labeling.<br> <Img Src="http://openwetware.org/images/5/58/S_Outside-gel-3.2.png" width="300"><br> Fig.5 Non-stained gel image: only bands in two lanes can be seen. From the left, they are DNA Origami with fluorescent molecules in pre-annealing (Ori*), and DNA Origami with fluorescent molecules in post-annealing (Ori**)<br> <br> In a stained gel (Fig.6), marker lane (lane 1) had the longest DNA strand of 20kb. Comparing this band and the band of M13mp18 (lane 2) with annealed DNA Origami (lane 3,4,5), the bands of the Origami are at the higher position. Therefore, we concluded that in lane3~5, DNA Origami structure was made as we had expected. <br> We considered that the bands in lane3~5 are seen as if they were diffused, just because our Origami has many staples binding to the fluorescent-tagged DNA, and each Origami attaches to different number of them, and its molecular weight varies.<br> <Img Src="http://openwetware.org/images/2/2d/S_Outside-gel-2.2.png" width="300"> </br> Fig.6 Stained gel image: from the left, marker, M13mp18, Ori*, Ori**, and DNA Origami with no fluorescent molecule (Ori)<br> <br>

<h6>Discussion</h6> Combining the results of Fig.5 and 6, the fluorescently labeled bands in lane3 and 4 in Fig.5 are at the same height as those of DNA Origami in Fig.6. Thus, we concluded our Origami was successfully fluorescently labeled.<br> <br>

<h5>2-1-3 Disrupting liposomes by DNA Origami<h5> <h6>Purpose</h6> To break liposomes with our Origami, first we investigate how our DNA Origami affect liposomes.<br> <br> <h6>Principle</h6> To break liposomes with our Origami, a lot of Origami has to hybridize to the surface of the liposomes.<br> To begin with, we added cholesterol-conjugated single-stranded DNA (in the rest of this document, referred to as Origami-anchor DNA) into liposomes, and made it float on the surface. The Origami-anchor DNA has a complementary part to our Origami, so the Origami is expected to hybridize to Origami-anchor DNA on the liposomes. In this way, lots of Origami would hybridize to liposomes via Origami-anchor DNA.<br> <br> <h6>Method</h6> We added Origami-anchor DNA into liposomes at the final concentration of 0.018, 0.069, 1.8, and 6.9µM. Then we observed the samples with a phase microscope. <br> Next, adding fluorescently labeled DNA Origami into the above liposomes, we saw if some change would happen with a fluorescent microscope.<br> <A href="http://openwetware.org/wiki/Biomod/2013/Sendai/protocol">Protocol</A><br> <br> <h6>Result</h6> In all four conditions, liposomes were observed with a phase microscope. We confirmed the formation of multi-lamella liposomes (Fig.7~10).<br> <br>

<!--ここは表を使ってコンパクトに-->

<Img Src="http://openwetware.org/images/7/72/Lipofig4.png" width="400"></br> Fig.7 Phase microscope image of liposomes (Origami-anchor DNA: 0.018µM)<br> <br> <Img Src="http://openwetware.org/images/d/d0/Lipofig5.png" width="400"></br> 

Fig.8 Phase microscope image of liposomes (Origami-anchor DNA: 0.069µM)<br>

<br> <Img Src="http://openwetware.org/images/d/de/Lipofig6.png" width="400"></br> 

Fig.9 Phase microscope image of liposomes (Origami-anchor DNA: 1.8µM)<br>

<br> <Img Src="http://openwetware.org/images/d/d7/Lipofig7.png" width="400"></br> 

Fig.10 Phase microscope image of liposomes (Orgami-anchor DNA: 6.9µM)<br>

<br> Adding fluorescently labeled DNA Origami into the above liposomes, we saw if some change would happen with a fluorescent microscope.<br> When the concentration of Origami-anchor DNA was 0.018, 0.069µM, many gleaming (in green color) liposomes were observed. We confirmed that the fluorescently labeled Origami well hybridized to the liposomal surface (Fig.11,12,13). <br> <table> 

<tr>
 <td>
  <Img Src="http://openwetware.org/images/6/6c/Lipofig8.png" width="400">
 </td>
 <td>
  <Img Src="http://openwetware.org/images/a/a6/Lipofig9.png" width="400">
 </td>
</tr>

</table> Fig.11,12 fluorescent microscope image of liposomes (Origami-anchor DNA: 0.018µM)<br> <Img Src="http://openwetware.org/images/b/b4/Lipofig10.png" width="400"></br> Fig.13 fluorescent microscope image of liposomes (Origami-anchor DNA: 0.069µM)<br> <br> On the other hand, when the concentration of Origami-anchor DNA was 1.8µM, few gleaming liposomes could be seen with a fluorescent microscope (Fig.14). This result indicates the possibility that liposomes have broken.<br> <Img Src="http://openwetware.org/images/1/18/Lipofig11.png" width="400"></br> Fig.14 fluorescent microscope image of liposomes (Origami-anchor DNA: 1.8µM)<br> <br> When the concentration of Origami-anchor DNA is 6.9µM, some liposomes were gleaming and others distorted, forming networks (Fig.15).<br>

<Img Src="http://openwetware.org/images/8/88/Lipofig12.png" width="400"></br> 

Fig.15 fluorescent microscope image of liposomes (Origami-anchor DNA: 6.9µM)<br>

<br> <h6>Discussion</h6> From these results, we put forward the following hypothesis about the interaction of DNA Origami and liposomes.<br> When the concentration of Origami-anchor DNA is low (0.018, 0.069µM), DNA Origami hybridizes to the surface of liposomes relatively stablely. When the concentration is middle (1.8µM), more DNA Origami hybridizes to the surface and loads on it. The liposomes become fragile and easy to break. When the concentration is high (6.9µM), some liposomes exist individually, and others form networks via Origami-anchor DNA and DNA Origami complex.<br> <Img Src="http://openwetware.org/images/7/7c/Experimentinsidefig.png"><br> <br> According to this hypothesis, when the concentration of Origami-anchor DNA is 1.8µM, DNA Origami breaks liposomes. <br> <br> <br>

<!-- 国内大会後の記事。国内大会前の結果の方がよかったからけしておく <h5>2-1-3 DNAオリガミによりリポソームを破壊する実験</h5> <h6>Purpose</h6> DNAオリガミによるアプローチではDNAオリガミがリポソーム表面にハイブリしてリポソームに負荷をかけて割れる。本実験ではDNAオリガミによってリポソームが割れるかどうかを確かめる。<br>

<h6>Method</h6>

DNAオリガミに蛍光をハイブリさせたものをアニーリングにより作製する<br> 界面通過法によりリポソームをつくる<br> 位相差顕微鏡でリポソーム2μℓを観察する（この時点ではまだ割れない）<br> 位相差顕微鏡で観察しているリポソーム2μℓにコレステロールレグ5μℓをピペッティングして混ぜ、観察する。（鍵DNAオリガミを入れていないのでこの時点ではまだ割れない）<br> 位相差顕微鏡で観察しているリポソーム＋コレステロールレグのサンプルに精製したDNAオリガミ4μℓを加え、顕微鏡で観察する<br>

Protocol （対応するプロトコルへのリンク）

<h6>Result</h6> リポソームのみの位相差顕微鏡の画像は図７のようになった。リポソームが確認できる。<br>

図７ リポソーム2μℓの位相差顕微鏡画像<br> リポソームにコレステロールレグを加えたサンプルの位相差顕微鏡画像は図８のようになった。この時点でもリポソームが確認できた。<br>

図８ リポソーム2μℓ+コレステロールレグ5μℓの位相差顕微鏡画像<br> リポソーム＋コレステロールレグに精製したDNAオリガミを加えた位相差顕微鏡画像は図９のようになった。DNAオリガミを加えた３分後にネットワークのような構造が確認された。このネットワーク構造はDNAオリガミを加える前は確認できなかったものである。<br>

図９ リポソーム2μℓ+コレステロールレグ5μℓ+精製したDNAオリガミ4μℓの位相差顕微鏡画像<br> <h6>Discussion</h6> このネットワーク構造はDNAオリガミを加えたあとに発生した。そのため、このネット―ワークのような構造はリポソームが割れた跡なのではないかと考えられる。<br> しかし、今回は顕微鏡で観察しているリポソームにコレステロールレグやDNAオリガミのサンプルを加えたためリポソームの濃度が薄くなるので一つのリポソームを定点観察することが難しく、リポソームが割れる瞬間を観察できなかった。<br> 浸透圧で割れない程度の粘性の高いリポソームやアガロースゲルで固定してリポソームを観察すれば定点観察できると考えられる。<br> -->

<h5>2-1-4 Confirming sequence specificity of DNA </h5> <h6>Purpose</h6> In this project, we adopt DNA for the Key of chain reaction because DNA has a significant characteristic: sequence specificity. Utilizing this sequence specificity, we aim to select liposomes that will be broken by Key DNA, induce chain-reactive liposomal disruption by some Key DNA, and make connections between liposomes.<br> Corresponding to the liposomes, we arrange two kinds of Origami-anchor DNA of different sequences and attach the anchor to the liposomes. Then we mix both kinds of liposomes together. <br> Into the mixture, Key DNA for just one kind of liposomes is added. We confirm that the Key DNA breaks only the corresponding kind of liposomes.<br> <br>

<h6>Method</h6> We made two kinds of liposomes: liposomeA and liposomeB by water-in-oil emulsion process. LiposomeA contains GFP (Green Fluorescent Protein) inside, and liposomeB has Rhodamine (red fluorescent dye) in itself. <br> <!--脂質の組成は？--> <br> Origami-anchor DNA for liposome A has the sequence of 5'-CCAGAAGACG-chol-3'. The anchor for liposome B has the sequence of 5'-TCCACTAACG-chol-3'. Both Origami-anchor DNA was mixed with the corresponding liposomes.<br> Each liposome was centrifuged for one minute to remove the excess Origami- anchor DNA.<br> Then we mixed 1µl of each liposome and observed it with a phase-contrast microscope. Next, 4µl refined DNA Origami was added to the mixture (of liposomeA and B). The sample was also observed with a phase-contrast microscope. <br> <!--蛍光ついている？？--> Protocol<br> （対応するプロトコルへのリンク）<br>

<h6>Result</h6> Fig.16 is the phase-contrast microscope image of the mixture of liposome A and B before the addition of Key DNA Origami. <br> <img src="http://openwetware.org/images/6/68/LegA%2BB_10.jpg"><br> Fig.16 Phase contrast microscope image of the mixture of liposome A (Green) and B (Red) <h6>Discussion</h6> (要加筆) <br> <h4>2-2 Flower DNA approach</h4> <h5> 2-2-1 Confirming the formation of the loop structure by SPR</h5> <h6>Purpose</h6> To break liposomes by flower DNA method, we aim to attach many loop strands to the surface of liposomes. <br> To achieve this, we adopt the same hybridization method via Anchored DNA as used in i)Bending approach into liposomes: the Anchored DNA has a complementary part to our loop strand and the loop strand is expected to hybridize to liposomes.<br> We checked the hybridization of liposomes and Anchored DNA, and that of Anchored DNA and our loop strands. <br> <br>

<h6>Principle</h6> As our loop strand is too small to observe with an AFM or a fluorescent microscope, we used an apparatus called SPR.<br> SPR is a Surface Plasmon Resonance assay that estimates the weight of molecules attached to membrane surface, by the change of the reflection of the laser beam.<br> If Anchored DNA attaches to a liposome, and then loop strand attaches to it, SPR value increases after each step.<br> We measured SPR value after each step of adding DOPC into liposomes, and loop DNA into it.<br> <br>

<h6>Method</h6> <ur><li>1. Inject 45µl DOPC (100mM) into SPR</li> <li>2. Inject 5µl NAOH to SPR in order to stabilize the point</li> <li>3. Inject 10µl Anchored DNA (0.1µM) to SPR</li> <li>4. Inject 10µl loop DNA of 40 bp (0.1µM) to SPR</li> <li>5. Inject 10 µl Key DNA of 40 bp (0.1µM) to SPR</li> <br> <br>

<h6>Result</h6> The result was shown in Fig.15 below.<br>

<Img Src="http://openwetware.org/images/f/fd/Flowerex2.png"></br> Fig.15 The transition of SPR value<br> <br> As the first injection of Anchored DNA caused no change of SPR value, we injected Anchored DNA for two times. <br> Fig 15 shows that SPR value increased after injecting Anchored DNA and loop DNA. Moreover, we should note that after injecting Key DNA some changes of SPR value were observed.<br> <br>

<h6>Discussion</h6> Fig.15 shows the behavior of materials on the surface of liposomes. The increase of SPR value after injecting Anchored DNA indicates that Anchored DNA successfully combined with liposomes. Similarly, it is considered that loop DNA combined with Anchored DNA. <br> Thus, we confirmed the formation of the loop structures on liposomes.<br> <br>

<h5>2-2-2フラワーミセルによりリポソームを破壊する実験</h5> <h6>Purpose</h6> In flower DNA approach, the Key DNA strand attaches to Flower-anchor DNA on liposomes, load on the liposomes, and break them. We confirm the disruption of liposomes フラワーミセルアプローチでは鍵DNAストランドがリポソーム表面に生えているアンカーDNAにハイブリしてリポソームが割れる必要がある。それを確かめるために。

<h6>Method</h6> We annealed DNA Origami with fluorescently labeled staples. Liposomes dyed with Texas Red (fluorescent dye) were prepared, and observed with a fluorescent microscope. Then we added DNA Origami into the liposomes. They were also observed with a fluorescent microscope. DNAオリガミに蛍光をハイブリさせたものをアニーリングにより作製する 膜染色（テキサスレッド）したリポソームをつくる リポソームのみを蛍光顕微鏡で観察する。 リポソームにDNAオリガミを加えてその後の様子を観察する （対応するプロトコルへのリンク）

<h6>Result</h6>

<h6>Discussion</h6>

<h5>2-2-3 DNAによる配列特異性を証明する実験</h5> <h6>Purpose</h6>

<h6>Method</h6> （対応するプロトコルへのリンク）

<h6>Result</h6>

<h6>Discussion</h6> 


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